In 2008, he batted .197 for Tampa Bay in 76 at bats. Ruggiano became part of a historical play in the 2008 World Series when Rays manager Joe Maddon moved Ruggiano from right field to become a fifth infielder, playing directly behind the second base bag.

On May 26, 2012, Ruggiano was traded to the Miami Marlins for minor league catcher Jobduan Morales.[3] He was called up to Miami the next day, and Kevin Mattison was optioned to Triple-A.[4] After playing well in June, Ruggiano heated up in July. He ended the first half of the season with 6 home runs (4 in the last 6 games), 17 RBIs, and a batting average of .390. On September 21, Ruggiano injured his shoulder in the fifth inning in agame against the New York Mets. He finished the season batting .313 with 13 homers, 36 RBIs, 23 doubles, a .374 on-base percentage(OBP), and a .909 on-base slug percentage(OPS).

On December 12, 2013, the Marlins traded Ruggiano to the Chicago Cubs for outfielder Brian Bogusevic. As a part-time outfielder during the 2014 season he played in 81 games before requiring surgery on his left ankle. Ruggiano finished the 2014 season hitting .281/.337/.429 in 224 at-bats, with six home runs and 28 RBIs.[5]

On December 17, 2014, he was traded to the Seattle Mariners in exchange for minor leaguer Matt Brazis.[6] He was designated for assignment on June 4, 2015. He cleared waivers and was assigned outright to the class AAA Tacoma Rainiers.